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IPBS Seminar Series - Deeper insight into viral infections

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Caroline Goujon

Institut de Recherche en Infectiologie de Montpellier (IRIM), France

The interferon inducible isoform of NCOA7 inhibits endosome-mediated viral entry

 

Type 1 interferon induces a potent antiviral state through the regulation of hundreds of interferon-stimulated genes (ISGs), with some acting broadly against multiple viruses while others display distinctive substrate specificity. Following interferon treatment, influenza A virus infection is largely inhibited, and both the MxA GTPase and the integral membrane protein IFITM3 contribute substantially to suppression. However, these ISGs do not fully account for the interferon-induced phenotype, and we have identified the short isoform of NCOA7 as a new ISG which plays an important role in influenza A virus restriction. CRISPR/Cas9 knock-out of NCOA7 partially rescues influenza A virus infection in the presence of interferon. Conversely, the ectopic expression of NCOA7 potently inhibits influenza A virus infection. Importantly, we have observed that hepatitis C virus, as well as VSV-G- and rabies-pseudotyped lentiviruses are also inhibited by NCOA7, in contrast to lentiviruses bearing their natural env glycoproteins, suggesting that this factor could prevent endosome-mediated entry of viruses. Step-wise dissection of influenza A virus entry demonstrated that NCOA7 does not prevent acid-induced conformational changes in the viral haemaglutinin (HA) but inhibits fusion of the viral and endosomal membranes and subsequent nuclear translocation of the viral ribonucleoproteins. Critically, combinations of knock-out and overexpression experiments have shown that IFITM3, which also acts at the level of viral entry, and NCOA7 are functionally independent. We have also shown that ectopic expression of this gene globally increases the pH of intracellular vesicles and the activity of lysosomal proteases. Finally, interactions with several cytoplasmic subunits of the vATPase and NCOA7 provide support for a model in which interferon-mediated regulation of the vacuolar H+ ATPase (vATPase) restricts influenza A virus infection.

Selected references

  • Doyle T, Goujon C and Malim MH (2015) HIV-1 and interferons: who's interfering with whom? Nat Rev Microbiol 13, 403-413
  • Goujon C et al. (2015) A triple-arginine motif in the amino-terminal domain and oligomerization are required for HIV-1 inhibition by human MX2. J Virol 89, 4676-4680
  • Goujon C et al. (2014) Transfer of the amino-terminal nuclear envelope targeting domain of human MX2 converts MX1 into an HIV-1 resistance factor. J Virol 88, 9017-9026
  • Goujon C et al. (2013). Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection. Nature 502, 559-562
  • Schaller T, Goujon C and Malim MH (2012) AIDS/HIV. HIV interplay with SAMHD1. Science 335, 1313-1314

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Mickaël Ménager

Institut Imagine, Paris, France

Network inference as a new approach to better understand transcriptomic pathways engaged upon dendritic cell response to HIV infection

 

HIV-1 in the presence of Vpx engages an intrinsic signaling response in human Dendritic Cells (DCs). It remains unclear how multiple transcription factors (TFs) downstream of innate immune sensing regulate the differential expression of hundreds of innate immune genes, production of type I interferon, and DC maturation. Under a spectrum of innate immune and viral perturbations, we used the power of machine learning algorithms (Inferelator) combined with the generation of “Big data” (Whole transcriptomic (RNA-seq) and chromatin accessibility changes (ATAC-seq)) to better understand how HIV-1 is sensed by human DCs and how this sensing by the innate immune system leads to type I IFN production and DC maturation. We have inferred a dynamic computational model that describes the molecular-level regulation of 542 TFs predicted to control the expression of 21,862 targets with close to 75,000 regulatory edges, following HIV-1 infection in human dendritic cells (Fig 1). Using a Louvain Modularity clustering algorithm, we partition the network into ten major TFs and gene target “neighbourhoods,” with three of these neighbourhoods populated with interferon regulator factors (IRFs), nuclear factor-kB (NF-kB) family members, and unexpected TFs that appear hyperactive during the innate response.  Validation of network nodes through genetic perturbation and RNA-sequencing on sorted cell populations reveals that separate TFs families control interferon production and DC maturation. This network highlights how the innate response depends on the coordinated action of multiple TFs and provides a resource for interrogation of key pathways that regulate HIV replication and innate immunity.

Selected references

  • Ménager MM and Littman DR (2016) Actin dynamics regulates dendritic cell-mediated transfer of HIV-1 to T cells. Cell 164, :695-709
  • Côte M*, Ménager MM* et al. (2009) Munc18-2 deficiency causes familial hemophagocytic lymphohistiocytosis type 5 and impairs cytotoxic granule exocytosis in patient NK cells. J Clin Invest 119, 3765-73
  • Ménager MM et al. (2007) Secretory cytotoxic granule maturation and exocytosis require the effector protein hMunc13-4. Nat Immunol 8, 257-67

Contact : Etienne Meunier (meunier@ipbs.fr) / Christel Verollet (verollet@ipbs.fr)

Note for visitors: Please come with a valid identity card

11 Dec

10:00 - 12:00

Seminar room - IPBS - Campus 205